CGSpace Notes

Documenting day-to-day work on the CGSpace repository.

March, 2024

in  Notes

2024-03-01

2024-03-03

  • I did some cleanups on abstracts, licenses, and dates from CrossRef
  • I also did some minor cleanups to affiliations because I saw some incorrect and duplicate ones in our list

2024-03-05

  • I tried a new technique to get some affiliations from Crossref using OpenRefine
    • First I split them and clustered, resolving a few hundred clusters out of 1500 (!)
    • Then I used a custom text facet with a few dozen CGIAR and other large affiliations to reduce the work
    • Then I joined them with our affiliations, paying no attention to duplicates
    • Then I deduped them using the Jython technique I learned in 2023-02

2024-03-06

  • Peter sent me some more corrections for the authors that I had sent him in 2023-12

2024-03-08

  • IFPRI sent me their 2023 records from CONTENTdm so I started working on those
    • I found a way to match their ORCID identifiers in our list using Jython in OpenRefine:
import re

with open(r"/tmp/cg-creator-identifier.txt",'r') as f :
    orcid_ids = [orcid_id.strip() for orcid_id in f]

matched = False
for orcid_id in orcid_ids:
    if re.search(r'.+: {}'.format(value), orcid_id):
        matched = True
        break

if matched:
    return orcid_id
else:
    return value

UPDATE metadatavalue SET text_value='United Nations Children''s Fund' WHERE dspace_object_id IN (SELECT uuid FROM item) AND text_value IN ('United Nations International Children''s Emergency Fund', 'United Nations International Children''s Emergency Fund', 'UNICEF');
  • Note the use of two single quotes to escape the one in the name

2024-03-11

  • Experimenting with moving some of my Python scripts to the DSpace 7 REST API
  • I spent some time working on the script get abstracts from CGSpace, and found a bug in my logic
    • I also noticed that one item had two abstracts, but the first one was blank!
    • Looking deeper, I found 113 blank metadata values so I deleted those:
BEGIN;
DELETE FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND text_value='';
COMMIT;
  • I also found a few dozen items with “N/A” for their citation, so I deleted those too:
BEGIN;
DELETE FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item) AND text_value='N/A' AND metadata_field_id=146;
COMMIT;
  • I deployed the change to disable Angular SSR’s inlineCriticalCss on production because we had heavy load on the frontend and I’ve been meaning to do this permanently for some time
  • Maria asked me for a CSV with all the broken Bioversity permalinks so I exported them for her:
$ csvcut -c 'id,dc.title[en_US],dc.identifier.uri[en_US],cg.link.permalink[en_US]' ~/Downloads/2024-03-05-cgspace.csv \
  | csvgrep -c 'cg.link.permalink[en_US]' -r '^.+$' > /tmp/2024-03-11-Bioversity-Permalinks.csv

2024-03-12

  • Run the duplicate checker for IFPRI 2023 batch upload

2024-03-13

  • I found about 428 duplicates in the IFPRI 2023 batch records
    • Alarmingly, I found about 18 that are duplicated on CGSpace as well!
    • I looked closer and decided that 11 were duplicates, so I merged the metadata and withdrew the later ones
  • Alliance asked me to get him the Handles for items submitted by TIP that are not discoverable 
SELECT ds6_item2itemhandle(dspace_object_id) AS handle FROM metadatavalue WHERE dspace_object_id IN (SELECT uuid FROM item WHERE NOT discoverable) AND metadata_field_id=28 AND text_value LIKE 'Submitted by Alliance TIP Submit%';

2024-03-14

  • Looking in to reports of rate limiting of Altmetric’s bot on CGSpace
    • I don’t see any HTTP 429 responses for their user agents in any of our logs…
    • I tried myself on an item page and never hit a limit…
$ for num in {1..60}; do echo -n "Request ${num}: "; curl -s -o /dev/null -w "%{http_code}" https://dspace7test.ilri.org/items/c9b8999d-3001-42ba-a267-14f4bfa90b53 && echo; done
Request 1: 200
Request 2: 200
Request 3: 200
Request 4: 200
...
Request 60: 200
  • All responses were HTTP 200…
  • In any case, I whitelisted their production IPs and told them to try again
  • I imported 468 of IFPRI’s 2023 records that were confirmed to not be duplicates to CGSpace
    • I also spent some time merging metadata from 415 of the remaining 432 duplicates with the metadata for the existing items on CGSpace
    • This was a bit of dirty work using csvkit, xsv, and OpenRefine

2024-03-17

  • There are 17 records from IFPRI’s 2023 batch that are remaining from the 432 that I identified as already being on CGSpace
    • These are different in that they are duplicates on CGSpace as well, so the csvjoin failed and the metadata got messed up in my migration
    • I looked closer and whittled this down to 14 actual records, and spent some time working on them
    • I isolated 12 of these items that existed on CGSpace and added publication ranks, project identifiers, and provenance links
    • Now there only remain two confusing records about the Inkomati catchment

2024-03-18

  • Checking to see how many IFPRI records we have migrated so far:
$ csvgrep -c 'dc.description.provenance[en_US]' -m 'Original URL from IFPRI CONTENTdm' cgspace.csv \
  | csvcut -c 'id,dc.title[en_US],dc.identifier.uri[en_US],dc.description.provenance[en_US],dcterms.type[en_US]' \
  | tee /tmp/ifpri-records.csv \
  | csvstat --count
898
  • I finalized the remaining two on Inkomati catchment and now we are at 900!

2024-03-19

  • IWMI sent me some new author ORCID identifiers so I updated our list
  • Started working on updating my data for the Ontology CoP webinar on CGIAR and AGROVOC
    • First extracting all unique subjects on CGSpace:
localhost/dspace7= ☘ \COPY (SELECT DISTINCT(lower(text_value)) AS "subject" FROM metadatavalue WHERE dspace_object_id in (SELECT dspace_object_id FROM item) AND metadata_field_id IN (187, 120, 210, 122, 215, 127, 208, 124, 128, 123, 125, 135, 203, 236, 238, 119)) to /tmp/2024-03-19-cgspace-subjects.csv WITH CSV HEADER;
COPY 28024
  • Then I extracted the subjects and looked them up against AGROVOC:
$ csvcut -c subject /tmp/2024-03-19-cgspace-subjects.csv | sed '1d' > /tmp/2024-03-19-cgspace-subjects.txt
$ ./ilri/agrovoc_lookup.py -i /tmp/2024-03-19-cgspace-subjects.txt -o /tmp/2024-03-19-cgspace-subjects-results.csv

2024-03-20

  • Identify seven duplicates on CGSpace from the PRMS results and withdraw them from CGSpace

2024-03-21

  • Look more closely at duplicates on CGSpace based on a fresh export
    • Using DOIs I found ~842 that occur more than once for journal articles alone, so probably around 400 duplicates
    • I did a handful of them, merging the metadata and withdrawing the duplicate, and decided to add dcterms.replaces with the handle in the original

2024-03-22

  • Look at duplicate DOIs on CGSpace and address a dozen or so

2024-03-23

  • Look at duplicate DOIs on CGSpace and address a dozen or so
  • Update Tomcat and Solr to latest versions
    • I had done some tests with these last week, and did a last minute test on DSpace 7 Test to make sure submission and searching worked

2024-03-24

  • Slowly process several dozen more duplicate DOIs on CGSpace, sigh…